The threat of destruction and plan to erase the crew memories only came about due to Data remaining conscious. That is not their usual M.O.
DATA
They are xenophobes, sir. Isolationists. The Paxans terraformed a protoplanet in this system in order to better conceal their whereabouts. The apparent wormhole we experienced is actually a trap designed to keep out invaders. The energy field stuns everyone on board the invading vessel and places them in a state of biochemical stasis. [...] The Paxans then take the ship out of their territory.
RIKER
So the crew wakes up and thinks they've been through a wormhole, count their blessings and keep going.
DATA
Precisely.
The choice they've given the crew TWICE is either to agree to a collective mind rape or be annihilated. You can't deny that, can you? How many times in your opinion should someone be guilty of rape before you call him a rapist? Plus we don't know how many of these "exceptions" to their MO they've effected before. It's likely that the people on whom their stun field doesn't work will be murdered without being even given another chance. That means they murder people who's only crimes are to be there and being resistant to their weapon. Why should the federation tolerate such a permanent threat to innocent passersby? Unless they are morally corrupt cowards that is, who are unwilling to fight for their principles.
I'll say if you have the pretense of maintaining peace in your corner of the Galaxy, you can't tolerate such people, so you must either control them or failing that, destroy them.